The comparison is apt, just not entirely. It isn't a comparison of IE6 vs Webkit, it's of developer reactions to them.
For a long time, IE6 ruled the roost, so developers used IE6 as their development target. Browsers that moved beyond it, or implemented things differently (often correctly) were ignored.
On mobile, webkit rules the roost. Developers use it as their development target. Browsers that move beyond it or implement things differently (by using non-webkit prefixed CSS) are ignored.
For a long time, IE6 ruled the roost, so developers used IE6 as their development target. Browsers that moved beyond it, or implemented things differently (often correctly) were ignored.
On mobile, webkit rules the roost. Developers use it as their development target. Browsers that move beyond it or implement things differently (by using non-webkit prefixed CSS) are ignored.